Fuller was a contemporary of Edward Montagu at the University of Cambridge and Pepys knew him personally, perhaps through that connection.

He supported the Royalist cause but also managed to maintain relationships with those on the Parliamentary side. His literary output was considerable. This is an extract from the Church History of Britain mentioned by Sam: http://www.la.utexas.edu/research/poltheory/ful...

This Thomas Fuller is footnoted for the Sept 23, 1664 entry in "The Diary of Samuel Pepys: 1664" (University of California Press, 1995, Robert Latham, William Matthews) "Thomas Fuller, Fellow of Christ's, 1649-61, was now Rector of Navenby, Lincs. As praevaricator he was a licensed jester at the disputation in philosophy, making learned but nonsensical play with the question under dispute. A sample of his wit (verses on {"An anima hominsis sit tabula rasa") is in W. T. Costello, "Scholastic curriculum at early 17th-cent." Cambridge, pp. 27-9. He was now interceding to protect a waterman from the press-gang..."

Further biographical information comes from the "Dictionary of National Biography" (Oxford, 1908, Leslie Stephen and Sidney Lee).

As part of the entry for this Thomas Fuller's uncle, also a clergyman named Thomas Fuller, (and said to be of the same family as the other church historian Thomas Fuller):"As bishop of Ardfert he (the uncle) ordained his three nephews, who all rose to some eminence, the sons of his brother John, who succeeded his fater as vicar of Stebbing: Thomas, fellow of Christ's College, Cambridge, an acquaintance of Pepys, mentioned several times in his 'Diary,' subsequently, in 1658, chaplain to Colonel Lockhart, governor of Dunkirk, vicar of the college living of Navenby, near Lincoln, and retor of Willingale Doe, Esses, 1670, 'an inveterate preferment hunter,' who died at Navenby in March 1701..."